[gmx-users] AGAIN fatal error:determinant in mdrun

[Osmany Guirola Cruz]

I have the same error in my simulation
i do a em step whitout problem but when i begin the md(whitout define = 
-DPOSRES)simulations i have problem whith Lincs
i probe use shake but the method not converge ,
Please  what i have to do whith my mdp files for a GREAT SIMULATION
    thanks

nanyu101 wrote:

>Dear gmx-users,
>  I have created a bigger lipid bilayer with genconf.
>genconf -f popc128a.pdb -nbox 2 2 1 -dist 0 0 0 -o popc.pdb
>
>And this bilayer is as big as four times of former bilayer.After doing that, I have run minimization for this big bilayer with cut-off for long distance electrostatic.
> title               =  Yo
>cpp                 =  /lib/cpp
>define              =  -DPOSRES
>constraints         =  none
>integrator          =  steep
>emstep              =  0.001
>emtol               =  10
>nsteps              =  200000
>nstcomm             =  1
>nstxout             =  50
>nstvout             =  1000
>nstfout             =  0
>nstlog              =  10
>nstenergy           =  10
>nstlist             =  10
>pbc                 =  xyz
>ns_type             =  grid
>coulombtype         =  cut-off
>rlist               =  1.2
>rcoulomb            =  1.8
>rvdw                =  1.4
>Tcoupl              =  no
>Pcoupl              =  no                              
>gen_vel             =  no
> 
>
>After minimizing my big bilayer,I tried to run NPT, but the system told me this:
>Using Gromacs SSE single precision assembly innerloops.
>
>           Step           Time         Lambda      Annealing
>              0        0.00000        0.00000        1.00000
>
>   Rel. Constraint Deviation:  Max    between atoms     RMS
>       Before LINCS         0.004860  47622  47624   0.000779
>        After LINCS         0.000078  19562  19563   0.000009
>
>Fatal error: Determinant = 1325213994729268314112.000000
>
>
>My operation mdp file and commands are listed as follows.
>cpp                 =  /lib/cpp
>define              =  -DPOSRES
>constraints         =  all-bonds
>integrator          =  md
>dt                  =  0.002	; ps !
>nsteps              =  10000
>nstcomm             =  1
>comm_mode           =  angular
>nstxout             =  50
>nstvout             =  1000
>nstfout             =  0
>nstlog              =  10
>nstenergy           =  10
>nstlist             =  10
>pbc                 =  xyz
>ns_type             =  grid
>coulombtype         =  cut-off
>fourierspacing      = 0.12
>optimize_fft        = yes
>rlist               =  1.0
>rcoulomb            =  1.8
>rvdw                =  1.4
>Tcoupl              =  no
>Pcoupl              =  berendsen
>pcoupltype          =  anisotropic                              
>tau_p               =  1   1   1   0   0   0
>compressibility     =  4.5e-5  4.5e-5  4.5e-5  0.0  0.0  0.0
>ref_p               =  1   1  1  0  0  0
>gen_vel             =  yes
>gen_temp            =  325.0
>gen_seed            =  1
> 
>
>editconf -f popc.pdb -o popc.gro
>editconf -bt cubic -f popc.gro -o popc.gro -c -center 0 0 0 -rotate 0 0 0
>grompp -f md.mdp -c popc.gro -p popc.top -o popc.tpr
>mdrun -v -deffmn popc
>
>
>Any comments are recommended. Thanks a lot.
>
>best wishes,
>Xianhui Wu
>
>
> 
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